Lonestar6 TACC/Unix Exercise

Get your data

Get set up

cds
cd my_rnaseq_course
cd day_1_partA/tacc_exercise

Exercise:

Run a simple command on each of these four files. We are going to just print the first 10 lines of each file.

First you need all the files. One is missing. Download it from here -> genes.1 and transfer it to your lonestar6 account (under day_1_partA/tacc_exercise)

Use the scp command from your computer (or winscp if its a windows machine)

#FOR MAC: 
#Open terminal
#Go to where genes.1 got downloaded (most likely Downloads)
cd ~/Downloads
scp genes.1 <username>@ls6.tacc.utexas.edu:/scratch/*/<username>/my_rnaseq_course/day_1_partA/tacc_exercise
#In case of corrupted MAC error, use the following option:
scp -o "MACs=hmac-sha2-512" genes.1 <username>@ls6.tacc.utexas.edu:/scratch/*/<username>/my_rnaseq_course/day_1_partA/tacc_exercise

#FOR WINDOWS:
Use winscp (free to download) to drag and drop the files from your computer to the server (in the right directory).

Make a commands file with the unix commands to print the first 10 lines of each file into an output file.

Open an editor to create a file called commands

Use head command to print the first 10 lines.

Use launcher_creator.py to create a launcher to submit this job (command file).

launcher_creator.py -h to see the options.

Submit the job.

Use our summer school reservation when submitting jobs to get higher priority:

sbatch --reservation=rna-seq-class-0609

sbatch

Check the queue.

showq -u <username>

Check the output files and log files.

Look at <jobname>.o* file for output information

Look at <jobname>.e* file for log/error information